nc.f: Nc vs. GC3s

In mariodosreis/tai: The tRNA adaptation index

Nc vs. GC3s

Description

Calculates the expected Nc value of a gene for a given GC content at the third codon positions.

Usage

nc.f(x)

Arguments

x	a vector of GC contents at third codon positions

Details

Without selection on codon bias, the expected value of Nc as a function of GC content at third positions, x, is given by

f(x) = -6 + x + 34/(x^2 + (1.025 - x)^2).

This equation follows dos Reis et al. (2004, see also Wright 1990 for the original).

Value

A vector of Nc values for the given GC contents.

Author(s)

Mario dos Reis

References

Wright F. (1990) The 'effective number of codons' used in a gene. Gene, 87: 23–9.

dos Reis M., Savva R., and Wernisch L. (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res., 32: 5036–44.

Examples

curve(nc.f(x), xlab="GC3s content", ylab="Nc")
points(ecolik12$w$GC3s, ecolik12$w$Nc, pch=19)

mariodosreis/tai documentation built on June 9, 2022, 7:37 p.m.